[Socbin] Postdoctoral Researcher: Algorithm and software development

[Johan Elf]

*Postdoctoral Researcher*
**
*Algorithm and software development for intracellular reaction - diffusion
kinetics*

We are seeking an outstanding postdoctoral researcher who will develop
algorithms and software for *multiscale simulation of stochastic*
*reaction-diffusion processes*.  The position is located within the Elf
and Lötstedt groups at Uppsala University in Sweden. See the homepages
http://www2.icm.uu.se/molbio/elflab/index.html and
http://www.it.uu.se/research/project/csbio

The purpose of the suggested project is to develop a new multiscale
algorithm for spatially heterogeneous systems by coupling the
macroscopic reaction-diffusion equations to mesoscopic simulation by the
multivariate master equation. The key to the method is to correctly and
efficiently sample the stochastic events from the time and space
dependent fields of reaction propensities that depend on both the
macroscopic and mesoscopic quantities.

The successful candidate will join an exciting collaboration between Elf
 lab, developing single molecule techniques and simulation methods to
study intracellular reactions and diffusion, and the Lötstedt group,
developing accurate and efficient numerical methods for studying
stochastic and dynamic systems. Some recent papers by the groups are
listed below.

Applicants must hold a recent PhD degree in scientific computing,
computational biology or a related subject. A prior experience of
working with partial differential equations, stochastic simulations,
kinetic modeling and software development with C/C++ would be highly
desirable.
Application procedures: Please upload (1) CV including list of
publications,(2)  short letter describing research interests (max half
A4) and (3) 2 letters of reference or contact information for two
references following the link at
http://www2.personalavd.uu.se/ledigaplatser/2506researcher.html

Feel free to contact Johan Elf (johan.elf at icm.uu.se) at the Department
of Cell and Molecular Biology or Per Lötstedt (perl at it.uu.se) at the
Department of Information Technology for more information.

Selected recent references:

·  Brian English, Vasili Hauryliuk, Arash Sanamrad, Stoyan Tankov, Nynke
Dekker, Johan Elf (2011) Single Molecule Investigations of the Stringent
Response Machinery in Living Bacterial Cells, PNAS
<http://www.pnas.org/content/108/31/E365.long>108(31):E365-73.

·  David Fange, Otto G. Berg, Paul Sjöberg, Johan Elf (2010) Modeling of
intracellular reaction-diffusion processes: Approaching the molecular
limit, PNAS <http://www.ncbi.nlm.nih.gov/pubmed/21041672>107:19820-5.

.  Lars Ferm, Andreas Hellander, Per Lötstedt (2010) An adaptive
algorithm for simulation of stochastic reaction-diffusion processes, J
Comput Phys, 229:343-360.

·  Andreas Grönlund, Per Lötstedt, Johan Elf (2010) The costs and
constraints from time-delayed feed-back in small gene regulatory motifs
PNAS <http://www.pnas.org/content/107/18/8171.abstract>107:8171-8176.

·  Andreas Grönlund, Per Lötstedt, Johan Elf (2011) Delay induced
anomalous fluctuations in intracellular regulation, Nature Commun.
<http://www2.icm.uu.se/molbio/elflab/references/natureComm2011.pdf>2:419.

 . Stefan Engblom, Lars Ferm, Andreas Hellander, Per Lötstedt (2009)
Simulation of stochastic reaction-diffusion processes on unstructured
meshes, SIAM J Sci Comput, 31:1774-1797.
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